#include <pbdata/sam/ReferenceSequence.hpp>

const char* SAMReferenceSequence::SAMReferenceSequenceFieldNames[] = {"SN", "LN"};

void SAMReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair>& kvPairs,
                                       uint64_t lineNumber)
{
    (void)(lineNumber);
    std::vector<bool> usedFields;
    usedFields.resize(SQ_LN);
    std::fill(usedFields.begin(), usedFields.end(), false);
    for (size_t i = 0; i < kvPairs.size(); i++) {
        if (kvPairs[i].key == "SN") {
            sequenceName = kvPairs[i].value;
            usedFields[SQ_SN] = true;
        } else if (kvPairs[i].key == "LN") {
            StoreValue(kvPairs[i].value, length);
            usedFields[SQ_SN] = true;
        }
    }
    for (size_t i = 0; i < usedFields.size(); i++) {
        if (usedFields[i] == false) {
            std::cout << "SQ specifier missing " << SAMReferenceSequenceFieldNames[i] << std::endl;
        }
    }
}

const char* SAMFullReferenceSequence::SAMFullReferenceSequenceFieldNames[] = {"AS", "M5", "SP",
                                                                              "UR"};

void SAMFullReferenceSequence::StoreValues(std::vector<SAMKeywordValuePair>& kvPairs,
                                           uint64_t lineNumber)
{
    SAMReferenceSequence::StoreValues(kvPairs, lineNumber);
    for (size_t i = 0; i < kvPairs.size(); i++) {
        if (kvPairs[i].key == "AS") {
            genomeAssembly = kvPairs[i].value;
        } else if (kvPairs[i].key == "M5") {
            md5 = kvPairs[i].value;
        } else if (kvPairs[i].key == "SP") {
            species = kvPairs[i].value;
        } else if (kvPairs[i].key == "UR") {
            uri = kvPairs[i].value;
        }
    }
}